Download Integration of telomere sequences with the draft human genome

letters to nature
chromosome clone containing the 14q telomere (F.M., unpublished data). The distance to the alphoid centromeric repeats is
unknown. However, the current most centromeric BAC already
extends 1,200 kb beyond the most proximal marker of previously
reported maps11–13. Interestingly, this clone contains two markers
from our TNG map that exhibit extremely high retention rates in
the hybrid lines, indicating that they may be close to the
centromere.
The clone coverage of chromosome 14 that has been achieved
using essentially an STC strategy is very satisfactory, and compares
favourably with the coverage obtained for the human chromosomes
that have been completely sequenced3,4. The two remaining gaps are
located in the subtelomeric part of 14q; subtelomeric regions of
many chromosomes are under-represented in most genomic
libraries and hence often contain cloning gaps. The largest gap,
estimated to be around 600 kb, was subsequently divided into two
smaller gaps following the identification of clones through library
screening with probes mapped within the gap. The second and more
distal gap (20 kb) occurs in the immunoglobulin heavy-chain
constant gene region, which contains a number of nearly identical
genes and pseudogenes.
Considerations of the optimum design of an STC strategy should
include theoretical aspects which correlate the effective depth of the
clone end library and the number of seed points to the level of
sequence redundancy10,14, as well as practical aspects such as the
sequencing capacity and costs15, the time schedule for the project
and the resolution of the available mapping data. However, a
centralized repository of BAC end sequences is the only prerequisite
for the construction of a tiling path based on the STC approach.
Other mapping resources used in this project were auxiliary and
provided useful information for seed selection and validation of
map extension. Such a strategy is therefore generally portable to any
large-scale sequencing project and is readily compatible with
partitioning of the project.
M
Received 20 October; accepted 21 December 2000.
1. Venter, J. C., Smith, H. O. & Hood, L. A new strategy for genome sequencing. Nature 381, 364–366
(1996).
2. Mahairas, G. G. et al. Sequence-tagged connectors: a sequence approach to mapping and scanning the
human genome. Proc. Natl Acad. Sci. USA 96, 9739–9744 (1999).
3. Dunham, I. et al. The DNA sequence of human chromosome 22. Nature 402, 489–495 (1999).
4. The chromosome 21 mapping and sequencing consortium. The DNA sequence of human chromosome 21. Nature 405, 311–319 (2000).
5. The International Human Genome Mapping Consortium. A physical map of the human genome.
Nature 409, 934–941 (2001).
6. Gyapay, G. et al. A radiation hybrid map of the human genome. Hum. Mol. Genet. 5, 339–346
(1996).
7. Soderlund, C., Longden, I. & Mott, R. FPC: a system for building contigs from restriction
fingerprinted clones. Comput. Appl. Biosci. 13, 523–535 (1997).
8. Agarwala, R., Applegate, D. L., Maglott, D., Schuler, G. D. & Schaffer, A. A. A fast and scalable
radiation hybrid map construction and integration strategy. Genome Res. 10, 350–364 (2000).
9. Lange, K., Boehnke, M., Cox, D. R. & Lunetta, K. L. Statistical methods for polyploid radiation hybrid
mapping. Genome Res. 5, 136–150 (1995).
10. Roach, J. C., Siegel, A. F., van den Engh, G., Trask, B. & Hood, L. Gaps in the Human Genome Project.
Nature 401, 843–845 (1999).
11. Dib, C. et al. A comprehensive genetic map of the human genome based on 5,264 microsatellites.
Nature 380, 152–154 (1996).
12. Deloukas, P. et al. A physical map of 30,000 human genes. Science 282, 744–746 (1998).
13. Dear, P. H., Bankier, A. T. & Piper, M. B. A high-resolution metric HAPPY map of human
chromosome 14. Genomics 48, 232–241 (1998).
14. Batzoglou, S., Berger, B., Mesirov, J. & Lander, E. S. Sequencing a genome by walking with clone-end
sequences: a mathematical analysis. Genome Res. 9, 1163–1174 (1999).
15. Siegel, A. F. et al. Analysis of sequence-tagged-connector strategies for DNA sequencing. Genome Res.
9, 297–307 (1999).
Supplementary information is available on Nature’s World-Wide Web site
(http://www.nature.com) or as paper copy from the London editorial office of Nature.
Acknowledgements
We thank D. Cox, P. Dear and D. Cox for unpublished data and helpful discussions.943
Correspondence and requests for materials should be addressed to R.H.
(e-mail: [email protected]).
948
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Integration of telomere sequences
with the draft human genome
sequence
H. C. Riethman*, Z. Xiang*, S. Paul*, E. Morse*, X.-L. Hu*, J. Flint†,
H.-C. Chi‡, D. L. Grady‡ & R. K. Moyzis‡
* The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104,
USA
† Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
‡ Department of Biological Chemistry, College of Medicine,
University of California, Irvine, California 92697, USA
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Telomeres are the ends of linear eukaryotic chromosomes. To
ensure that no large stretches of uncharacterized DNA remain
between the ends of the human working draft sequence and the
ends of each chromosome, we would need to connect the
sequences of the telomeres to the working draft sequence. But
telomeres have an unusual DNA sequence composition and
organization that makes them particularly difficult to isolate
and analyse. Here we use specialized linear yeast artificial chromosome clones, each carrying a large telomere-terminal fragment
of human DNA, to integrate most human telomeres with the
working draft sequence. Subtelomeric sequence structure appears
to vary widely, mainly as a result of large differences in subtelomeric repeat sequence abundance and organization at individual
telomeres. Many subtelomeric regions appear to be gene-rich,
matching both known and unknown expressed genes. This indicates that human subtelomeric regions are not simply buffers of
nonfunctional ‘junk DNA’ next to the molecular telomere, but are
instead functional parts of the expressed genome.
Telomeres are essential for genome stability and faithful chromosome replication. The chromatin structures associated with telomeric DNA mediate the many biological activities associated with
telomeres, including cell-cycle regulation, cellular ageing, movement and localization of chromosomes within the nucleus, and
transcriptional regulation of subtelomeric genes1,2. Specialized
functions involving telomeric and subtelomeric DNA have evolved
in several eukaryotes. For example, frequent subtelomeric gene
conversion provides diversity for surface antigens in trypanosomes3,
and rapidly evolving subtelomeric gene families confer selective
advantages for closely related yeast strains4.
Human telomeres end with a stretch of the conserved simple
repeat sequence (TTAGGG)n5. This tract is present at the end of all
telomeres and therefore cannot be used to distinguish one telomere
from another. To capture single-copy human DNA regions linked to
telomeres that are useful for this purpose, we isolated large telomere-terminal fragments of human chromosomes using specialized
yeast artificial chromosome (YAC) cloning vehicles called halfYACs6. Each half-YAC clone contains a large segment of subtelomeric DNA flanked by the cloning vector sequence at one end and
the human telomere repeat sequence, which has been modified to
operate as a functional yeast telomere in vivo, at the other. Characterization of these clones revealed low-copy subtelomeric repeats
adjacent to the (TTAGGG)n sequence6,7. Physical mapping experiments on a large group of these half-YAC clones showed that, in
most cases, they can stably maintain faithful copies of human
telomere-terminal DNA fragments in yeast8. By contrast, bacterial
artificial chromosome (BAC) libraries used to prepare the human
working draft sequence are not expected to contain sequences
extending to the telomere, owing to the absence of restriction
sites in (TTAGGG)n, the effects of length associated with the
construction of size-selected DNA recombinant clones, and the
genomic instability of these regions9.
© 2001 Macmillan Magazines Ltd
NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com
letters to nature
We used a combination of chromosome-specific single-copy
sequences derived from the half-YAC clones and DNA end sequence
derived from cosmid subclones of the half-YACs to connect most
telomeres to the working draft sequence (Fig. 1). Our results show
that the working draft sequence includes remarkably good coverage
of human telomere regions. For the 24 human chromosomes, we
analysed 46 telomere ends in all. The telomeres of the sex chromosome pair X and Y recombine meiotically, so these four telomeres
are treated as two (designated the Xp/Yp pseudoautosomal telomere and the Xq/Yq pseudoautosomal telomere). We could integrate the working draft sequence with 32 telomere regions captured
by half-YAC clones (blue dots). Of these 32 regions, 18 have working
draft sequence coverage that includes DNA less than 50 kilobases
(kb) from the telomere; for five of them, the sequence extends to the
terminal (TTAGGG)n sequences10–13 (see Supplementary Information). Although we were unable to capture two telomeres (5p and
20q) in half-YAC clones, we identified these regions in subtelomeric
repeat-containing BAC clones and used them to connect to the
working draft sequence (green dots).
We were unable to connect 7 of the remaining 12 telomere ends to
the working draft, either because the working draft sequence does
not yet extend into these regions (2q, 7p, 17p, 17q and Xp/Yp) or
because unambiguous identification of overlapping working draft
sequence was prevented by repeat sequences in the telomere clones
(19p and 19q). BAC or cosmid clones connected to each of these
seven telomeres were identified during construction of the fingerprint-based clone map of the human genome14 (http://genome.wustl.edu/gsc/human/Mapping/index.shtml) and this is likely to
facilitate the future integration of these telomeres into the working
draft (see Methods). The five acrocentric chromosomes (13, 14, 15,
21 and 22) contain heterochromatic short arms comprising
repeated DNA. We did not analyse these five short-arm telomeres
(black rectangles) because their sequences were unstable in
both yeast and bacteria, rendering them difficult to clone and
characterize.
We have made available a detailed summary of the mapping
experiments integrating telomeres with the working draft sequence,
including specific telomere reagents, working draft contig designations, individual BAC clone accessions and accession numbers for
our half-YAC-derived sequences (see Supplementary Information).
For some chromosome ends, such as that of 11p (Fig. 2), we could
precisely estimate the distance between the end of the working draft
sequence and the telomere. However, this was not the case for many
telomeric regions because much of the working draft sequence is
still in small, unordered pieces.
As part of this study, around 1.1 megabases (Mb) of half-YACderived DNA sequence was acquired from cosmid end sequencing
as well as from draft and finished sequencing of some subtelomeric
cosmids (see Supplementary Information). In addition to defining
the overlap relationship between the working draft sequence and the
telomere clones, the half-YAC-derived sequences were useful for
sampling the subtelomeric regions not yet included in the working
draft sequence but captured in the half-YAC clones. Preliminary
analysis of the half-YAC-derived sequences and the regions of the
working draft sequence that overlapped with the half-YACs revealed
several interesting features.
The sizes of subtelomeric repeat regions adjacent to the terminal
(TTAGGG)n varied widely among individual telomeres, from 8 kb
at the 7q telomere to ,300 kb at the 8p telomere. Large variations in
subtelomeric repeat content have been detected near at least 18
telomeres8,15,16. Nonetheless, the scale of human genomic subtelomeric repeat content is now well defined, and it is clear that a
significant part of the subtelomeric repeat region of the human
genome is present in the working draft sequence.
Large subtelomeric repeat regions can cause false linkages in the
CEN
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Figure 1 Summary of integration of telomeric DNA with working draft sequence. The two
human pseudoautosomal telomere pairs (Xp/Yp and Xq/Yq) each recombine meiotically,
so each pair is treated as a single telomere. Blue: the working draft sequence extends into
these 32 telomere regions defined by half-YAC clones. Green: the working draft sequence
ends within these subtelomeric repeat regions, but the distance to the molecular telomere
is not known. Red: the telomeric DNA has not yet been integrated with working draft
sequence. Telomere clones for the five acrocentric short-arm regions (black rectangles)
have not been characterized.
NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com
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Figure 2 Connecting the 11p telomere to the working draft sequence. The end of the
working draft sequence is represented by fragment AF015416 (magenta rectangle; a
constitutent of working draft contig 18272). The half-YAC clone yRM2209 (black) is
represented below. Cosmid subclones were derived from the half-YAC clone and the
contig of these subclones, which encompasses most of the half-YAC clone, was aligned
by EcoRI restriction sites (small vertical marks). The cosmid end sequences (yellow
triangles) were screened to the working draft sequence to orient the clones relative to the
11p telomere. This physical mapping enabled us to determine the size and features of the
45-kb telomeric region missing from the working draft sequence. Features include a 25kb region of subtelomeric repeat DNA (green), an internal (TTAGGG)n telomere repeat
sequence (red) and four Unigene clusters of ESTs (blue dots). Within the 140-kb region
extending from the telomere, we determined the location of three known genes, IFITM2
(an interferon-induced transmembrane protein), PSMD13 (a component of the
proteasome 26S subunit) and SIRT3 (a Sir-2-like histone deactylase implicated in
telomere maintanance), as well as the positions of unigene clusters of ESTs that match
11ptel sequences and are distinct from known genes (blue dots).
© 2001 Macmillan Magazines Ltd
949
letters to nature
BAC map and misassembly of working draft sequence. Large
stretches of low-copy repeat DNA from subtelomeric repeat regions
also localize to some pericentric chromosome regions, to the shortarm heterochromatin of acrocentric chromosomes and to a few loci
in internal regions of chromosomes (for example, 1q42, 2q31, 4q28,
12p12 and Yq11.2). In previous iterations of the BAC map there
were many instances of incorrect merges of subtelomeric repeatcontaining BACs. To help identify these potentially problematic
regions of the BAC map and working draft sequence, we have
catalogued individual BAC clones containing segments of
similarity with subtelomeric repeat regions (http://www.wistar.
upenn. edu/Riethman). Inconsistencies between the current version
of the BAC accession map (http://genome.wustl.edu:8021/pub/
gsc1/ fpc_files/ freeze_2000_10_07/MAP/) and our telomere mapping studies are indicated in the Supplementary Information.
The abundance of low-copy repeat regions near telomeres is likely
to make whole-genome shotgun assembly of subtelomeric regions
virtually impossible. Indeed, previously characterized Drosophila
subtelomeric repeat sequences are absent from its genome
sequence17. By contrast, the entire sequence of yeast telomeric and
subtelomeric regions was acquired using the half-YAC cloning
strategy employed here18.
Internal telomere-like sequences, each consisting of around 50–
250 base pairs (bp) of a mixture of perfect and imperfect copies of
(TTAGGG)n11, were present in all subtelomeric repeat regions
analysed. For example, multiple copies of internal telomere-like
sequences were present in widely spaced parts of the 100-kb 18p
subtelomeric repeat region, and were present in both orientations
relative to the telomere. It is interesting to speculate that packaging
of subtelomeric chromatin might involve interactions between the
terminal (TTAGGG)n repeats and these internal telomere
sequences. The TRF1 protein, which binds to (TTAGGG)n in vivo
and can bind sequences corresponding to the short internal
repeats in vitro19, would be a good candidate for mediating such
interactions.
Preliminary analysis of the potential gene content of the subtelomeric regions encompassed by the half-YAC-derived sequences
and the overlapping portions of the subtelomeric working draft
sequence was done by searching for sequence matches between the
genomic DNA sequences and potential gene-derived complementary DNA and expressed sequence tag (EST) sequences in GenBank
(http://www.wistar.upenn.edu/Riethman). Even this preliminary
analysis reveals two features of subtelomeric regions. First, there
are many sequence matches with genes and ESTs in most subtelomeric regions. We detected about 500 matches to transcripts
identified by either a full-length cDNA or by a unigene cluster of
expressed sequences in the 40 telomere regions analysed; 62 of these
were found from half-YAC sequences mapping distal to the working
draft sequence. Second, many of the genes and potential genes
identified by sequence matches are members of gene families with
many pseudogene copies. The sequence matches included around
100 known genes, both unique and members of gene families.
Human subtelomeric sequences have been proposed to serve as a
buffer between the terminal (TTAGGG)n sequences, which are
needed to protect chromosome ends from fusion and recombination, and vital internal chromosomal sequences15. However, the
many expressed sequences throughout subtelomeric regions,
extending almost to the molecular telomere, suggest that these
regions may serve essential functions and are not simply dispensable
junk DNA.
M
Methods
We used a range of half-YAC-derived probes, including PCR- and cosmid subclone-derived
probes and sequences (see Supplementary Information) and sets of collaboratively derived
subtelomeric molecular and cytogenetic markers for specific telomeres20–22, to connect
specific cloned chromosome ends with flanking BAC contigs, either by DNA hybridization
and PCR experiments or by computer-based matches (using BLAST223 sequence alignment
programs) of sequenced subtelomeric DNA with working draft sequence.
950
Single-copy probes from three of the seven telomeres not connected to working draft
sequence could be used to identify BAC clones from an 11× coverage RP11 BAC library,
although fewer clones than expected were identified (singleton BACs from the 2q and the
17p telomeres, and three BACs from the 7p telomere). Low-copy repeat sequences at the
19p, 19q and 17q telomeres complicated attempted BAC library screens for these
chromosome ends, but independent experiments have identified PAC and BAC clones
connected to the 17q telomere22 and a detailed physical map of chromosome 19 (http://
greengenes.llnl.gov/genome/) exists to help guide closure of the 19p and 19q subtelomeric
gaps, which occur in duplicated regions containing a family of zinc finger-encoding genes.
The remaining telomere region (Xp/Yp) is encompassed by a 500-kb clone contig
extending to within a few kb of the telomere24.
Physical mapping experiments using a site-specific cleavage method (RARE cleavage8,25)
have been done for 21 telomeres to demonstrate co-linearity of the half-YAC insert DNA
with the cognate telomere. In the absence of RARE cleavage data, the presence of
subtelomeric repeats adjacent to terminal (TTAGGG)n sequences in all of the designated
half-YAC clones is taken as strong evidence for proximity to the telomere; this has been
borne out by the RARE cleavage experiments carried out so far.
Half-YAC clones containing chromosome-specific DNA were not recovered from four
chromosome ends. BAC and cosmid clones identified by virtue of their subtelomeric
repeat content form the initial basis for the telomere linkages to 5p, 20q, 19q and Xp/Yp.
The BAC clones used to mark the 5p and 20q telomeres and the cosmid used to mark the
19q telomere each contain an internal telomere repeat sequence and subtelomeric repeat
sequences, and localize to telomeric ends of the BAC map (5p, 20q) and the chromosome
19 physical map (http://greengenes.llnl.gov/genome/). On the basis of the known
sequence organization of other telomeres, only additional subtelomeric repeat sequence is
likely to reside distal to the subtelomeric repeat segments contained in these clones,
although the possibility of single-copy DNA distal to them cannot be formally excluded at
present. A cosmid clone mapped to the Xp/Yp pseudoautosomal telomere using Bal31
exonuclease experiments26 forms the telomeric boundary of a large cosmid contig24 whose
sequence is not yet available.
Received 15 November; accepted 18 December 2000.
1. Blasco, M. A., Gasser, S. M. & Lingner, J. Telomeres and telomerase. Genes Dev. 13, 2353–2359
(1999).
2. deLange, T. & Jacks, T. For better or worse? Telomerase inhibition and cancer. Cell 98, 273–275 (1999).
3. McCulloch, R., Rudenko, G. & Borst, P. Gene conversions mediating antigenic variation in
Trypanosoma brucei can occur on variant surface glycoprotein expression sites lacking 70-bp repeat
sequences. Mol. Cell Biol. 17, 833–843 (1997).
4. Carlson, M., Celenza, J. L. & Eng, F. J. Evolution of the dispersed SUC gene family of Saccharomyces by
rearrangements of chromosomal telomeres. Mol. Cell Biol. 5, 2894–2902 (1985).
5. Moyzis, R. K. et al. A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres
of human chromosomes. Proc. Natl Acad. Sci. USA 85, 6622–6626 (1988).
6. Riethman, H. C., Moyzis, R. K., Meyne, J., Burke, D. T. & Olson, M. V. Cloning human telomeric DNA
fragments into Saccharomyces cerevisiae using a yeast-artificial-chromosome vector. Proc. Natl Acad.
Sci. USA 86, 6240–6244 (1989).
7. Brown, W. R. A. et al. Structure and polymorphism of human telomere-associated DNA. Cell 63, 119–
132 (1990).
8. Macina, R. A. et al. Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q
telomeres. Genome Res. 5, 225–232 (1995).
9. Doggett, N. A. et al. An integrated physical map of human chromosome 16. Nature 377 (Suppl.), 335–
365 (1995).
10. Flint, J. et al. The relationship between chromosome structure and function at a human telomeric
region. Nature Genet. 15, 252–257 (1997).
11. Flint, J. et al. Sequence comparison of human and yeast telomeres identifies structurally distinct
subtelomeric domains. Hum. Mol. Genet. 6, 1305–1313 (1997).
12. Ciccodicola, A. et al. Differentially regulated and evolved genes in the fully sequenced Xq/Yq
pseudoautosomal region. Hum. Mol. Genet. 9, 395–401 (2000).
13. Hattori, M. et al. The DNA sequence of human chromosome 21. Nature 405, 311–320 (2000).
14. The International Human Genome Mapping Consortium. A physical map of the human genome.
Nature 409, 934–941 (2001).
15. Wilkie, A. O. M. et al. Stable length polymorphism of up to 260 kb at the tip of the short arm of human
chromosome 16. Cell 64, 595–606 (1991).
16. Trask, B. J. et al. Members of the olfactory receptor gene family are contained in large blocks of DNA
duplicated polymorphically near the ends of human chromosomes. Hum. Mol. Genet. 7, 13–26 (1998).
17. Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–95 (2000).
18. Louis, E. J. & Borts, R. A complete set of marked telomeres in Saccharomyces cerevisiae for physical
mapping and cloning. Genetics 139, 125–136 (1995).
19. Bianchi, A. et al. TRF1 binds a bipartite telomeric site with extreme spatial flexibility. EMBO J. 18,
5735–5744 (1999).
20. Ning, Y. et al. A complete set of human telomeric probes and their clinical application. Nature Genet.
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21. Rosenberg, M. et al. Characterization of short tandem repeats from thirty-one human telomeres.
Genome Res. 7, 917–923 (1997).
22. Knight, S. J. L. et al. An optimized set of human telomere clones for studying telomere integrity and
architecture. Am. J. Hum. Genet. 67, 320–332 (2000).
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© 2001 Macmillan Magazines Ltd
NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com
letters to nature
We thank J. Finklestein, N. Atigapramoj, E. Dabagyan, S. Huang, A. Ambriz, A. Harxhi and
K. Sutton for their contributions to this work, which was supported by NIH and DOE.
Correspondence and requests for materials should be addressed to H.C.R.
(e-mail: [email protected]).
.................................................................
Comparison of human genetic and
sequence-based physical maps
Adong Yu*, Chengfeng Zhao*, Ying Fan*, Wonhee Jang†,
Andrew J. Mungall‡, Panos Deloukas‡, Anne Olsen§,
Norman A. Doggettk, Nader Ghebranious*, Karl W. Broman¶
& James L. Weber*
* Center for Medical Genetics, Marshfield Medical Research Foundation,
Marshfield, Wisconsin 54449, USA
† National Center for Biotechnology Information, National Institutes of Health,
Bethesda, Maryland 20894, USA
‡ The Sanger Centre, Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
§ Joint Genome Institute, Walnut Creek, California 94598, USA
k Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
¶ Department of Biostatistics, Johns Hopkins University, Baltimore,
Maryland 21205-2179, USA
.................................. ......................... ......................... ......................... ......................... ........
Recombination is the exchange of information between two
homologous chromosomes during meiosis. The rate of recombination per nucleotide, which profoundly affects the evolution of
chromosomal segments, is calculated by comparing genetic and
physical maps. Human physical maps have been constructed using
cytogenetics1, overlapping DNA clones2 and radiation hybrids3;
but the ultimate and by far the most accurate physical map is the
actual nucleotide sequence. The completion of the draft human
genomic sequence4 provides us with the best opportunity yet to
compare the genetic and physical maps. Here we describe our
estimates of female, male and sex-average recombination rates for
about 60% of the genome. Recombination rates varied greatly
along each chromosome, from 0 to at least 9 centiMorgans per
megabase (cM Mb−1). Among several sequence and marker parameters tested, only relative marker position along the metacentric
chromosomes in males correlated strongly with recombination
rate. We identified several chromosomal regions up to 6 Mb in
length with particularly low (deserts) or high (jungles) recombination rates. Linkage disequilibrium was much more common and
extended for greater distances in the deserts than in the jungles.
All nucleated human cells contain two homologous copies of each
chromosome, except for the sex chromosomes in males. During the
formation of the sperm and egg cells, the number of each chromosome is reduced to one so that fertilization restores the normal
diploid number in the next generation. The process of chromosome
reduction, meiosis, is usually accompanied by exchange or recombination of DNA between the homologous parental chromosomes.
Genetic maps, which are based on meiotic recombination, order
and estimate distances between DNA sequences that vary between
parental homologues (polymorphisms). The primary unit of distance along the genetic maps is the centiMorgan (cM), which is
equivalent to 1% recombination.
The genetic maps used in our analysis were based upon the
genotyping of 8,031 short tandem repeat polymorphisms (STRPs)
NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com
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Acknowledgements
from Généthon, the University of Utah and the Cooperative Human
Linkage Center in eight reference CEPH families5. Excluding the sex
chromosomes, the maps cover about 4,250 cM in females and
2,730 cM in males. The genetic maps are relatively marker dense,
with an average of 2–3 STRPs per cM, but are also relatively low
resolution because only 184 meioses (92 in each sex) were analysed.
The physical maps used were all DNA sequence assemblies. For
chromosomes 21 and 22, we used the finished, published sequences6,7.
For the other 20 autosomes and for the X chromosome, we used the
public draft sequence assemblies, 5 September 2000 version (http://
genome.cse.ucsc.edu)4. As we required relatively long stretches of
sequence, we used only sequence assemblies that were over 1.5 Mb
long (between terminal STRPs), contained more than three STRPs
and had a marker order that agreed with published genetic and
radiation hybrid maps. The amount of sequence used from each
chromosome is shown in Fig. 1. Some chromosomes had much
better coverage than others. We analysed 253 sequence assemblies
ranging in length up to 70 Mb and spanning a total of 1,806 Mb
(roughly 58% of the portion of the genome that is not highly
repetitive). By far the most common reason for rejecting sequence
assemblies was insufficient length; only seven assemblies were
rejected for incompatible marker order.
Recombination rates varied greatly across the genome, from 0 to
8.8 cM Mb−1 (Table 1). Sex-average recombination rates (the average for males and females combined) did not vary as much as the
sex-specific rates (for males and females considered separately)
because male and female recombination rates at specific sites
often differed substantially. We identified 19 recombination deserts
up to 5 Mb in length with sex-average recombination rates below
0.3 cM Mb−1, and 12 recombination jungles up to 6 Mb in length
with sex-average recombination rates greater than 3.0 cM Mb−1 (see
Supplementary Information). Wide variation in recombination
rates across chromosomes has been observed previously for
humans8–11 and for other eukaryotic species12–15, and is clearly the
rule rather than the exception.
In an effort to identify the basis of differences in recombination
rates, we compared the rates to several marker and sequence
parameters. These parameters included GC content, STRP informativeness, position of the marker relative to the centromeres and
telomeres, density of runs of various short tandem repeats, especially (A)n, (AC)n, (AGAT)n, (AAN)n and (AAAN)n sequences, and
the density of various interspersed repetitive elements, including
Length of sequence analysed (Mb)
Supplementary information is available on Nature’s World-Wide Web site
(http://www.nature.com) or as paper copy from the London editorial office of Nature.
10
0
0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
Chromosome
Figure 1 Sequence coverage for comparison of the genetic and physical maps. The total
length of sequence used in the analysis (open bars) and the approximate percentage of
the euchromatic sequence length (solid bars) are shown for each chromosome.
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